Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYOD1

Cell type

Cell type Class
Muscle
Cell type
RH-4
NA
NA

Attributes by original data submitter

Sample

source_name
RH4
cell line
RH4
antibody
MYOD
antibody vendor/catalog
Cell Signaling, 13812 (D8G3)
geo_loc_name
missing
collection_date
missing

Sequenced DNA Library

library_name
GSM6626416
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For spike-in normalized ChIP-seq, human RMS cells and mouse C2C12 cells were fixed in 1% formaldehyde for 10 minutes before quenching with 125 mM glycine. Cells were combined in a ratio of 3 human:1 mouse cell equivalents for each experiment prior to sonication. Sonicated chromatin was immunoprecipitated with antibodies against H3K27ac (Active Motif #39133), H3K9me3 (Active Motif #39062), MYOD1 (CST #13812), or CTCF (Millipore #07-729). Input and ChIP-enriched DNA was decrosslinked and purified using Qiagen MinElute PCR Purification columns prior to library preparation. H3K27ac, MYOD1, and CTCF ChIP and Input DNA libraries were prepared by blunt end repair using the Lucigen End-It DNA End-Repair Kit, 3' A-tailing by Klenow fragment (3'-5' exo-) (NEB), adaptor ligation by T4 DNA ligase(NEB), and size selection on an E-Gel 2% EX agarose gel. Libraries were amplified with barcoded primers and isolated from unreacted primers by gel purification. Decrosslinked H3K9me3 ChIP and Input DNA was sonicated to enrich fragments 200-500-bp. Library prep was then performed without further size selection. Excess adapter and unused primers were removed with AmpureXP beads. Libraries were sequenced on the HiSeq4000 or NovaSeq6000 platform running in PEx150bp mode.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
49554933
Reads aligned (%)
78.8
Duplicates removed (%)
1.9
Number of peaks
39998 (qval < 1E-05)

hg19

Number of total reads
49554933
Reads aligned (%)
78.3
Duplicates removed (%)
1.9
Number of peaks
39231 (qval < 1E-05)

Base call quality data from DBCLS SRA